Minister for Agriculture Michael Creed has said he does not accept that the Mercosur trade agreement is a "done deal" and it has not been approved by any government or parliament.
Speaking in the Dáil, Minister Creed said, "I consider there to be a considerable distance to travel before we have an inked deal that bears the imprimatur of Europe".
"What we have is a proposed deal," he added.
He said was "very disappointed" that the deal "contains a significant tariff rate quota that would allow the importation of beef from Mercosur to the European Union at preferential tariff rates.
He added that he was concerned that this was happening at a time when the beef sector is facing "significant uncertainty" due to Brexit.
Mr Creed was asked about the agreement by a number of Fianna Fáil TDs during a Topical Issues debate in the Dáil this evening.
Fianna Fáil's agriculture spokesperson Charlie McConalogue said the deal is "disastrous" for the Irish beef sector as it "makes no sense".
He said that Europe has enough beef and bringing in more will cause difficulties. He was critical that beef produced on the other side of the world would be shipped into the EU and this would have much more of a carbon footprint.
His party colleague Bobby Aylward said Brexit will have a serious impact on Irish farmers and they will not survive with Mercosur coming down the road.
Deputy Aylward asked for the Government to seek that the EU will hold off on the deal until it was known what was going to happen with Brexit.
Tipperary TD Jackie Cahill said farmers were angry about the challenge that is being put before them in terms of climate change while beef is now going to be imported from the other side of the world.
He accused the European Commission of "selling out our beef industry".
Responding, Minster Creed said the Mercosur agreement marks the end of 20 years of negotiations between the two trading blocs.
He said that the Government had worked hard with other member states to mitigate the potential impact of the deal on EU agriculture.
He also pointed out that the beef tariff rate quota agreed is considerably less than that originally sought by the Mercosur countries.
Meanwhile, speaking following the EU Leaders' summit in Brussels this evening, Taoiseach Leo Varadkar said Ireland would not back Mercosur deal if it was not in our interest.
He said: "What we have at the moment is a political agreement. It will be two years before we see the legal text and we vote on it. Whatever happens, I want to make sure our beef farmers are protected.
"That means insisting that the food safety and traceability standards are at a European level for any South American beef coming into Europe.
"It means insisting that this is linked to South American countries honouring their climate change obligations under Paris, and also insisting there is compensation for farmers, perhaps by opening up other markets."